{"id":394,"date":"2025-09-15T19:57:11","date_gmt":"2025-09-15T19:57:11","guid":{"rendered":"https:\/\/groups.chem.cmu.edu\/bier\/?page_id=394"},"modified":"2026-02-23T21:44:39","modified_gmt":"2026-02-23T21:44:39","slug":"lab-guides","status":"publish","type":"page","link":"https:\/\/groups.chem.cmu.edu\/bier\/resources\/lab-guides\/","title":{"rendered":"Lab Guides\/Group Member Resources"},"content":{"rendered":"<div class=\"et_pb_section_0 et_pb_section et_section_regular et_block_section\">\n<div class=\"et_pb_row_0 et_pb_row et_block_row\">\n<div class=\"et_pb_column_0 et_pb_column et_pb_column_2_3 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_0 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><h2><span style=\"text-decoration: underline;\">Resources<\/span><\/h2>\n<h2 style=\"text-align: left;\"><strong>Lab Guides\/Group Member Resources<\/strong><\/h2>\n<\/div><\/div>\n<\/div>\n\n<div class=\"et_pb_column_1 et_pb_column et_pb_column_1_3 et-last-child et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_1 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><h2 style=\"text-align: left;\">Bier Research Group<\/h2>\n<h3 style=\"text-align: left;\">Department of Chemistry<\/h3>\n<\/div><\/div>\n<\/div>\n<\/div>\n<\/div>\n\n<div class=\"et_pb_section_1 et_pb_section et_pb_fullwidth_section et_section_regular et_block_section\">\n<div class=\"et_pb_fullwidth_image_0 et_pb_fullwidth_image et_pb_module\"><\/div>\n<\/div>\n\n<div class=\"et_pb_section_2 et_pb_section et_section_regular et_block_section\">\n<div class=\"et_pb_row_1 et_pb_row et_pb_equal_columns et_block_row\">\n<div class=\"et_pb_column_2 et_pb_column et_pb_column_1_2 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_2 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><h3>SIMION 3D Version 7.0 User's Manual<\/h3>\n<ul>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_TOC.pdf\" target=\"_blank\" rel=\"noopener\">Table of Contents<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch1-Overview.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 1 - SIMION 3D Version 7.0 Overview<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch2-Basics.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 2 - SIMION Basics<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch3-UsefulDirections.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 3 - Useful Directions<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch4-Creating-Loading-Saving-PAs.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 4 - Creating, Loading, &amp; Saving Potential Arrays<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch5-Defining-Editing-Array-Geometry.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 5 - Defining &amp; Editing Array Geometry<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch6-Refining-Fast-Adjusting-Arrays.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 6 - Refining &amp; Fast Adjusting Arrays<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch7-Positioning-Viewing-Arrays-In-Workbench.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 7 - Positioning &amp; Viewing Arrays in the Workbench<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch8-Flying-Ions.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 8 - Flying Ions<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_Ch9-Advanced-Strategies-Tactics.pdf\" target=\"_blank\" rel=\"noopener\">Ch. 9 - Advanced Strategies &amp; Tactics<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixA.pdf\" target=\"_blank\" rel=\"noopener\">Appendix A - Hardware &amp; Software Requirements<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixB.pdf\" target=\"_blank\" rel=\"noopener\">Appendix B - Installing\/Troubleshooting SIMION 7.0<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixC.pdf\" target=\"_blank\" rel=\"noopener\">Appendix C - Sample SIMION 7.0 Runs<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixD.pdf\" target=\"_blank\" rel=\"noopener\">Appendix D - Files Used by SIMION 7.0<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixE.pdf\" target=\"_blank\" rel=\"noopener\">Appendix E - Computational Methods<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixF.pdf\" target=\"_blank\" rel=\"noopener\">Appendix F - SIMION's GUI<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixG.pdf\" target=\"_blank\" rel=\"noopener\">Appendix G - Printing Options<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixH.pdf\" target=\"_blank\" rel=\"noopener\">Appendix H - The EDY Survival Manual<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixI.pdf\" target=\"_blank\" rel=\"noopener\">Appendix I - User Programming<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixJ.pdf\" target=\"_blank\" rel=\"noopener\">Appendix J - Geometry Files<\/a> [.pdf]<\/li>\n<li><a href=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/SIMION7_AppendixK.pdf\" target=\"_blank\" rel=\"noopener\">Appendix K - Differences Between Versions 7.0 &amp; 6.0<\/a> [.pdf]<\/li>\n<\/ul>\n<\/div><\/div>\n<\/div>\n\n<div class=\"et_pb_column_3 et_pb_column et_pb_column_1_2 et-last-child et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_3 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><h3>Guides<\/h3>\n<ul>\n<li><a href=\"http:\/\/www.the-scientist.com\/?articles.view\/articleNo\/42261\/title\/Riding-Out-Rejection\/\" target=\"_blank\" rel=\"noopener\">The Scientist - Riding Out Rejection<\/a><\/li>\n<\/ul>\n<h3>Lab Management &amp; Safety<\/h3>\n<ul>\n<li><a href=\"https:\/\/cmu.bioraft.com\" target=\"_blank\" rel=\"noopener\">BioRAFT<\/a><\/li>\n<li><a href=\"https:\/\/chemtracker.stanford.edu\/ct\/?account=ct_cmu&amp;state=login\" target=\"_blank\" rel=\"noopener\">??ChemTracker<\/a><\/li>\n<li><a href=\"http:\/\/calendar.chem.cmu.edu\/chem\" target=\"_blank\" rel=\"noopener\">Bier Group Calendar<\/a> [Login required]<\/li>\n<\/ul>\n<h3>Mass Spectrometry Websites<\/h3>\n<ul>\n<li><a href=\"http:\/\/www.asms.org\" target=\"_blank\" rel=\"noopener\">American Society for Mass Spectrometry<\/a><\/li>\n<\/ul>\n<h3>Journals<\/h3>\n<ul>\n<li><a href=\"http:\/\/www.springer.com\/chemistry\/analytical+chemistry\/journal\/13361\" target=\"_blank\" rel=\"noopener\">Journal of the American Society for Mass Spectrometry<\/a><\/li>\n<li><a href=\"http:\/\/onlinelibrary.wiley.com\/journal\/10.1002\/(ISSN)1097-0231\" target=\"_blank\" rel=\"noopener\">Rapid Communications in Mass Spectrometry<\/a><\/li>\n<li><a href=\"http:\/\/onlinelibrary.wiley.com\/journal\/10.1002\/(ISSN)1096-9888c\" target=\"_blank\" rel=\"noopener\">Journal of Mass Spectrometry<\/a><\/li>\n<li><a href=\"http:\/\/www.journals.elsevier.com\/international-journal-of-mass-spectrometry\/\" target=\"_blank\" rel=\"noopener\">International Journal of Mass Spectrometry<\/a><\/li>\n<li><a href=\"http:\/\/pubs.acs.org\/journal\/ancham\" target=\"_blank\" rel=\"noopener\">Analytical Chemistry<\/a><\/li>\n<li><a href=\"http:\/\/pubs.acs.org\/journal\/jacsat\" target=\"_blank\" rel=\"noopener\">Journal of the American Chemical Society<\/a><\/li>\n<li><a href=\"http:\/\/www.sciencemag.org\/magazine\" target=\"_blank\" rel=\"noopener\">Science<\/a><\/li>\n<li><a href=\"http:\/\/www.nature.com\" target=\"_blank\" rel=\"noopener\">Nature<\/a><\/li>\n<li><a href=\"http:\/\/onlinelibrary.wiley.com\/journal\/10.1002\/(ISSN)1521-3773\" target=\"_blank\" rel=\"noopener\">Angewandte Chemie International Edition<\/a><\/li>\n<\/ul>\n<\/div><\/div>\n<\/div>\n<\/div>\n<\/div>\n\n<div class=\"et_pb_section_3 et_pb_section et_section_regular et_block_section\">\n<div class=\"et_pb_row_2 et_pb_row et_pb_equal_columns et_block_row\">\n<div class=\"et_pb_column_4 et_pb_column et_pb_column_1_3 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_4 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><h3>Mark E. Bier<\/h3>\n<p>Research Professor and Director, <a href=\"http:\/\/www.chem.cmu.edu\/cma\/\" target=\"_blank\" rel=\"noopener\">Center for Molecular Analysis<\/a><\/p>\n<\/div><\/div>\n<\/div>\n\n<div class=\"et_pb_column_5 et_pb_column et_pb_column_1_3 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_5 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><p><a href=\"mailto:mbier@andrew.cmu.edu\">mbier@andrew.cmu.edu<\/a><br \/>\n\t\t\t\t412-268-3540 (office)<br \/>\n\t\t\t\t412-268-1061 (fax)<br \/>\n\t\t\t\tOffice: MI 555<\/p>\n<\/div><\/div>\n<\/div>\n\n<div class=\"et_pb_column_6 et_pb_column et_pb_column_1_3 et-last-child et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_6 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><p><a href=\"http:\/\/www.chem.cmu.edu\/\" target=\"_blank\" rel=\"noopener\">Department of Chemistry<\/a><br \/><a href=\"http:\/\/www.cmu.edu\/\" target=\"_blank\" rel=\"noopener\">Carnegie Mellon University<\/a><br \/>Mellon Institute<br \/>4400 Fifth Ave., Pittsburgh, PA 15213<\/p>\n<\/div><\/div>\n<\/div>\n<\/div>\n<\/div>\n\n<div class=\"et_pb_section_4 et_pb_section et_section_regular et_block_section\">\n<div class=\"et_pb_row_3 et_pb_row et_block_row\">\n<div class=\"et_pb_column_7 et_pb_column et_pb_column_4_4 et-last-child et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_text_7 et_pb_text et_pb_bg_layout_light et_pb_module et_block_module\"><div class=\"et_pb_text_inner\"><p style=\"text-align: center;\">Our research is supported by the <strong>Berkmann Fund<\/strong>, <a href=\"http:\/\/www.cmu.edu\/uro\/index.html\" target=\"_blank\" rel=\"noopener\">CMU URO SURG &amp; SURF programs<\/a> and<\/p>\n<\/div><\/div>\n<\/div>\n<\/div>\n\n<div class=\"et_pb_row_4 et_pb_row et_pb_row_5col et_block_row et_block_row_5col\">\n<div class=\"et_pb_column_8 et_pb_column et_pb_column_1_5 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_image_0 et_pb_image et_pb_module et_block_module\"><span class=\"et_pb_image_wrap\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-hhmi.png\" width=\"101\" height=\"25\" srcset=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-hhmi.png 101w\" sizes=\"(max-width: 101px) 100vw, 101px\" class=\"wp-image-36\" title=\"logo-hhmi\" alt=\"HHMI logo\" \/><\/span><\/div>\n<\/div>\n\n<div class=\"et_pb_column_9 et_pb_column et_pb_column_1_5 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_image_1 et_pb_image et_pb_module et_block_module\"><span class=\"et_pb_image_wrap\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-nsf.png\" width=\"70\" height=\"71\" srcset=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-nsf.png 70w\" sizes=\"(max-width: 70px) 100vw, 70px\" class=\"wp-image-37\" title=\"logo-nsf\" alt=\"NSF logo\" \/><\/span><\/div>\n<\/div>\n\n<div class=\"et_pb_column_10 et_pb_column et_pb_column_1_5 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_image_2 et_pb_image et_pb_module et_block_module\"><span class=\"et_pb_image_wrap\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-fordfoundation.png\" width=\"300\" height=\"39\" srcset=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-fordfoundation.png 300w\" sizes=\"(max-width: 300px) 100vw, 300px\" class=\"wp-image-35\" title=\"logo-fordfoundation\" alt=\"Ford Foundation logo\" \/><\/span><\/div>\n<\/div>\n\n<div class=\"et_pb_column_11 et_pb_column et_pb_column_1_5 et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_image_3 et_pb_image et_pb_module et_block_module\"><span class=\"et_pb_image_wrap\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-cmu_stack.png\" width=\"69\" height=\"45\" srcset=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/logo-cmu_stack.png 69w\" sizes=\"(max-width: 69px) 100vw, 69px\" class=\"wp-image-34\" title=\"logo-cmu_stack\" alt=\"Carnegie Mellon University logo\" \/><\/span><\/div>\n<\/div>\n\n<div class=\"et_pb_column_12 et_pb_column et_pb_column_1_5 et-last-child et_block_column et_pb_css_mix_blend_mode_passthrough\">\n<div class=\"et_pb_image_4 et_pb_image et_pb_module et_block_module\"><span class=\"et_pb_image_wrap\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/scott_unitmark.png\" width=\"900\" height=\"244\" srcset=\"https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/scott_unitmark.png 900w, https:\/\/groups.chem.cmu.edu\/bier\/wp-content\/uploads\/sites\/12\/2025\/09\/scott_unitmark-480x130.png 480w\" sizes=\"(min-width: 0px) and (max-width: 480px) 480px, (min-width: 481px) 900px, 100vw\" class=\"wp-image-38\" title=\"scott_unitmark\" alt=\"Scott Institute for Energy Innovation logo\" \/><\/span><\/div>\n<\/div>\n<\/div>\n<\/div>","protected":false},"excerpt":{"rendered":"","protected":false},"author":21,"featured_media":0,"parent":344,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-394","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/pages\/394","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/users\/21"}],"replies":[{"embeddable":true,"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/comments?post=394"}],"version-history":[{"count":8,"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/pages\/394\/revisions"}],"predecessor-version":[{"id":570,"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/pages\/394\/revisions\/570"}],"up":[{"embeddable":true,"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/pages\/344"}],"wp:attachment":[{"href":"https:\/\/groups.chem.cmu.edu\/bier\/wp-json\/wp\/v2\/media?parent=394"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}